2011/3/25 Jason Grout <jason-s...@creativetrax.com>:
> On 3/25/11 7:03 PM, William Stein wrote:
>>
>> Hi,
>>
>> Please find bugs in http://flask.sagenb.org. Is it slow? Fast?
>> Broken in *any* way at all?
>
>
> Jmol doesn't work, as far as we can tell. We aren't sure why, though. Kudos
> to whoever can figure out why jmol isn't working!
>
> It seems that the jmol applet loads, but it can't find the file containing
> the jmol instructions, for some reason. It may be that what we really
> should do is just port the new jmol patch up on trac to work on this new
> server.
In case it helps, I see this on console:
-%<-
java version "1.6.0_20"
OpenJDK Runtime Environment (IcedTea6 1.9.7) (mandriva-16.b20-x86_64)
OpenJDK 64-Bit Server VM (build 19.0-b09, mixed mode)
Exception in thread "Thread-6" java.lang.NullPointerException
at sun.applet.AppletPanel.showAppletStatus(AppletPanel.java:947)
at sun.applet.AppletPanel.run(AppletPanel.java:607)
at java.lang.Thread.run(Thread.java:636)
urlImage=jar:file:/home/pcpa/.icedteaplugin/cache/http/flask.sagenb.org/java/jmol/JmolApplet0.jar!/jmol75x29x8.gif
Jmol applet jmolApplet0__7259920705109835__ initializing
AppletRegistry.checkIn(jmolApplet0__7259920705109835__)
applet context: -applet
appletDocumentBase=http://flask.sagenb.org/doc/live/tutorial/
appletCodeBase=http://flask.sagenb.org/java/jmol/
(C) 2008 Jmol Development
Jmol Version 11.6.16 2008-11-24 13:39
java.vendor:Sun Microsystems Inc.
java.version:1.6.0_20
os.name:Linux
memory:33.7/91.0
useCommandThread: false
appletId:jmolApplet0__7259920705109835__
FileManager opening http://flask.sagenb.org/java/jmol/appletweb/SageMenu.mnu
defaults = "Jmol"
backgroundColor = "black"
language=pt_BR
FileManager opening
http://flask.sagenb.org/home/_sage_/1/cells/14/sage0-size500.jmol?1301150152
script compiler ERROR: esperado um comando
----line 1 command 1 of /home/_sage_/1/cells/14/sage0-size500.jmol?1301150152:
>>>> <!DOCTYPE html> <<<<
ERRO no "script": script compiler ERROR: esperado um comando
----line 1 command 1 of /home/_sage_/1/cells/14/sage0-size500.jmol?1301150152:
>>>> <!DOCTYPE html> <<<<
eval ERROR:
----line 1 command 1:
script >> "/home/_sage_/1/cells/14/sage0-size500.jmol?1301150152" <<
-%<-
But testing on chromium-browser, firefox frequently is "more compatible".
I solved a similar issue of jmol not understanding the input in the mandriva
sagemath package, but for console use, by running "jmol -s", important
bits should be:
-%<-
--- sage-4.6.2/spkg/build/sage-4.6.2/sage/plot/plot3d/base.pyx.orig
2011-01-14
18:06:01.349974001 -0200
+++ sage-4.6.2/spkg/build/sage-4.6.2/sage/plot/plot3d/base.pyx 2011-01-14
18:07:03.463973996 -0200
@@ -817,12 +817,7 @@ end_scene""" % (render_params.antialiasi
return box_min, box_max
def _prepare_for_jmol(self, frame, axes, frame_aspect_ratio,
aspect_ratio, zoom):
- from sage.plot.plot import EMBEDDED_MODE
- if EMBEDDED_MODE:
- s = 6
- else:
- s = 3
- box_min, box_max =
self._rescale_for_frame_aspect_ratio_and_zoom(s, frame_aspect_ratio,
zoom)
+ box_min, box_max =
self._rescale_for_frame_aspect_ratio_and_zoom(6, frame_aspect_ratio,
zoom)
a_min, a_max = self._box_for_aspect_ratio(aspect_ratio,
box_min, box_max)
return self._transform_to_bounding_box(box_min, box_max,
a_min, a_max, frame=frame,
axes=axes, thickness=1,
@@ -1110,7 +1105,7 @@ end_scene""" % (render_params.antialiasi
T = self._prepare_for_jmol(frame, axes,
frame_aspect_ratio, aspect_ratio, zoom)
T.export_jmol(archive_name, force_reload=EMBEDDED_MODE,
zoom=zoom*100, **kwds)
- viewer_app = "sage-native-execute " +
os.path.join(sage.misc.misc.SAGE_LOCAL, "bin/jmol")
+ viewer_app = "jmol -s"
# We need a script to load the file
f = open(filename + '.jmol', 'w')
-%<-
While not exactly solving the issue, I hope this information may
help find the cause,
but the -s flag should only be required for newer jmol.
> And congrats to Mike, Rado, the many testers, and others who got this all
> working! It will be *much* easier to understand and modify the notebook
> code after we migrate to this.
>
> Thanks,
>
> Jason
Paulo
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